1 Reads only.2 Supported CHP files for import include: Affymetrix GCOS files, Affymetrix GCCC (Calvin) files, "Quantification-only" CHP files that are the result of doing PLIER or RMA normalization on Affymetrix .cel files, "Whole-transcript” CHP files that contain information for whole-transcript arrays3 To be readable in ArrayStar, the MAGE-ML *.dtd file must be present in the same folder as the Attributes file.4 Contains un-normalized signal data from Affymetrix. In order to interpret and normalize data from .cel files, ArrayStar requires a .cdf file (for 3’ expression chip types) or a .pgf file (for whole-transcript arrays). 5 Contains data from one chip with one or two color channels.6 ArrayStar does not support ABI files without base calls.
7 ArrayStar does not recognize features saved in *.mseq files as annotations.
8 Template only.
9 Contains data from one chip with two color channels. When importing *.gpr files, ArrayStar uses the linear values from the “Ratio of Medians” column as the signal intensity values.
10 Imported from HapMap via the Data Import Wizard.
11 See ArrayStar Help for more information.12 Contains either gene-level data (“Group Gene Profile” or “Sample Gene Profile”) or probe-level data (“Group Probe Profile” or “Sample Probe Profile”).13 Any user-defined, comma-delimited text files containing annotation or expression data. 14 Any user-defined text files containing annotation or expression data.15 Contains expression data for single or multiple chips.16 NimbleGen CALL-type files in TXT format. "NimbleGen Sample Key" is a type of Attributes file. For microarray projects, Attributes files may contain expression data for single or multiple chips.17 An unnormalized file with probe level data.18 Includes SNP data plus detailed feature, MID-tag, and sample name information.19 Created by opening a SeqMan NGen *.assembly in SeqMan Pro and exporting SNP data. The resulting *.txt file contains SNP data, as well as basic MID-tag and feature information. 20 Created in SeqMan Pro, or obtained via free download from the 1100 Genomes Project and the NHLBI Exome Sequencing Project (ESP).

Exported File Types

File Format

File Extension(s)

Variants

Microarray

QSeq (ChIP-Seq, CNV,miRNA, RNA-Seq)

Affymetrix CHP files / Normalized Signal Values

*.chp

✓

✓

✓

ArrayStar and QSeq projects

*.dmaproj,*.astar

✓

✓

✓

BED files1

*.bed

✓

GenBank files

*.gbk, *.gb

✓2

General Feature Format files1

*.gff

✓

GenVision projects3

*.gnv, *.txt

✓

Misc. comma-separated files4

*.csv

✓

✓

✓

Misc. text files4

*.txt

✓

✓

✓

Roche NimbleGen files5

*.txt

✓

✓

✓

Template and sequence files

*.fas

✓

Wiggle files3

*.wig

✓

1 Must be selected in Configure Advanced Options before processing.2 Template only.3 Export is in a graph format. Must be selected in Configure Advanced Options before processing.4 Only available in Gene Table view.5 NimbleGen CALL-type files in TXT format.